Mapping the genomic organization of modified histones and defining locations of deoxyribonucleic acid (DNA) binding proteins is important for understanding the regulatory mechanisms governing cellular states. The primary methodology used for mapping DNA associated proteins—chromatin immunoprecipitation followed by sequencing (ChIP-seq)—has several major limitations: (i) the ChIP-seq signal is effectively an average derived from a population of cells due to chromatin input requirements; (ii) standard ChIP-seq is unable to profile more than one epitope at one time in one sample; and (iii) the immunoprecipitation step is inefficient, resulting in signal reduction.